I don't think the atom number is the problem. I also have systems with more
than 99999 atoms, and in the gro file the atom number after 99999 is reset
to 0, but that was never a problem for the simulations. I would check the
parameters again, but I don't have a more exact answer to your problem.
2010/3/5 Carla Jamous <carlajamous at gmail.com>
> Hi,
> please I'm having a problem while running a minimisation.
>> I prepared my system with pdb2gmx and generated .pdb files. From the last
> pdb file, I did grompp & generated the tpr file that I used to start my
> minimization. At the 46th step, I encountered the problem:"water molecule
> cannot be settled".
> I looked at the pdb file and found that many water residues have the same
> number because above residue 9999, it restarts to count residue 0, 1, etc...
>> I prepared the same system but I generated .gro files instead of .pdb &
> started my minimization. But did't encounter the same problem.
> I looked at the gro file & here, it's the atomic number that can't be above
> 99999.
>> So did anyone encounter this problem before, & if yes, please do you have a
> solution to propose?
>> Thanks
>> Carla
>>> --
> gmx-users mailing list gmx-users at gromacs.org>http://lists.gromacs.org/mailman/listinfo/gmx-users> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php>-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100305/7364cf7c/attachment.html>